5R9S

PanDDA analysis group deposition Form1 MAP kinase p38-alpha -- Fragment N13470a in complex with MAP kinase p38-alpha


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.929127.5% PEG3350, 0.1 M Bis-Tris propane, pH 6.9, 50 mM ammonium sulfate, 0.2 M 1:1 magnesium chloride:magnesium sulfate, 10% glycerol
Crystal Properties
Matthews coefficientSolvent content
3.0459.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.785α = 90
b = 86.041β = 90
c = 127.473γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-02-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92819DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.729.2998.40.060.0650.0250.99919.66.655358
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7495.10.8230.8910.3390.7096.73912

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 6SO11.729.352548275797.990.18140.18050.1986RANDOM26.622
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.05-0.010.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.714
r_dihedral_angle_4_deg17.615
r_dihedral_angle_3_deg16.765
r_dihedral_angle_1_deg6.453
r_mcangle_it3.459
r_mcbond_other1.972
r_mcbond_it1.957
r_angle_refined_deg1.599
r_angle_other_deg1.354
r_chiral_restr0.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.714
r_dihedral_angle_4_deg17.615
r_dihedral_angle_3_deg16.765
r_dihedral_angle_1_deg6.453
r_mcangle_it3.459
r_mcbond_other1.972
r_mcbond_it1.957
r_angle_refined_deg1.599
r_angle_other_deg1.354
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2746
Nucleic Acid Atoms
Solvent Atoms238
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing